Cohesin chromatin loop formation by an extrinsic motor

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 30, 2023

Abstract The ring-shaped cohesin complex topologically entraps two DNAs to establish sister chromatid cohesion 1–3 . Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation 4–7 , which is thought achieve by actively extruding DNA loops without entrapping 8–11 ‘loop extrusion’ hypothesis finds motivation from in vitro observations 12–14 – whether this process underlies vivo loop formation remains untested. Here, using budding yeast S. cerevisiae we generate variants that have lost their ability extrude but retain entrap DNA. Analysis of these suggests form independently extrusion. Instead, find transcription promotes formation, as well acts an extrinsic motor expands and defines ultimate positions. Our results necessitate a re-evaluation extrusion model point alternative mechanism cohesin-dependent organisation. We propose cohesin, akin establishment at replication forks, forms DNA-DNA capture places transcription, thus unifying cohesin’s roles chromosome segregation genome

Language: Английский

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DNA-directed termination of mammalian RNA polymerase II

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

ABSTRACT The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage the nascent RNA. RNAPII-associated product is then degraded by XRN2, dislodging RNAPII from DNA template. In contrast, prokaryotic RNAP and RNAPIII often terminate directly at T-tracts in coding strand. Here, we demonstrate a similar omnipresent capability for mammalian RNAPII. XRN2- T-tract-dependent are independent - latter usually acting when XRN2 cannot be engaged. We show that snRNA transcription, previously thought to require Integrator complex. Importantly, find genome-wide promoter-proximal regions, but not within protein-coding gene bodies. XRN2-dependent dominates downstream genes, T-tract process sometimes employed. Overall, global DNA-directed attrition suggesting RNAPs retain potential over T-rich sequences throughout evolution.

Language: Английский

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Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Sept. 8, 2024

Language: Английский

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DNA-directed termination of mammalian RNA polymerase II

Genes & Development, Journal Year: 2024, Volume and Issue: 38(21-24), P. 998 - 1019

Published: Nov. 1, 2024

The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination involves polyadenylation site-directed cleavage the nascent RNA. RNAPII-associated product is then degraded by XRN2, dislodging RNAPII from DNA template. In contrast, prokaryotic RNAP and RNAPIII often terminate directly at T-tracts in coding strand. Here, we demonstrate a similar omnipresent capability for mammalian RNAPII. Importantly, this does not require upstream cleavage. Accordingly, T-tract-dependent can take place when XRN2 cannot be engaged. We show that snRNA transcription independently Integrator complex. found genome-wide promoter-proximal regions but within protein-coding gene bodies. XRN2-dependent dominates downstream genes, T-tract process sometimes used. Overall, global DNA-directed attrition transcription, suggesting RNAPs retain potential to over T-rich sequences throughout evolution.

Language: Английский

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DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 16, 2023

SUMMARY The timely termination of RNA polymerase II (Pol II) transcription is critical for recycling and preventing interference with the expression neighbouring genes. Termination Pol involves exoribonucleolytic decay nascent by 5’-3’ exonuclease Xrn2. Xrn2 attacks 5’-PO 4 -end executes degradation generated endonucleolytic cleavage at poly(A) site which eventually leads to release from DNA. However, molecular details when how during this process interacts elongation complex mediate its dissociation DNA not understood. Here, we demonstrate that Spt5, a conserved factor controls processivity pausing. Importantly, activity stimulated Spt5 in vitro Spt5-depleted cells show defective termination. Our results support model where first forms stable elongating acquire full degrading RNA. also promotes premature attenuating non-coding transcripts. By contrast, depletion retention promoters protein-coding IIs transcribe into gene body absence exhibit severely reduced rates pre-mRNA processing. We propose plays major role production functional mRNA directly stimulating enzymes entry complexes configured processing elongation.

Language: Английский

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Transcription elongation of the plant RNA polymerase IV is prone to backtracking

Science Advances, Journal Year: 2024, Volume and Issue: 10(34)

Published: Aug. 23, 2024

RNA polymerase IV (Pol IV) forms a complex with RNA-directed 2 (RDR2) to produce double-stranded (dsRNA) precursors essential for plant gene silencing. In the “backtracking-triggered channeling” model, Pol backtracks and delivers its transcript’s 3′ terminus RDR2, which synthesizes dsRNA. However, mechanisms underlying backtracking protection from cleavage are unclear. Here, we determined cryo–electron microscopy structures of elongation complexes at four states nucleotide addition cycle (NAC): posttranslocation, guanosine triphosphate–bound, pretranslocation, backtracked states. The reveal that maintains an open DNA cleft kinked bridge helix in all NAC states, loosely interacts nucleoside triphosphate substrate, barely contacts proximal nucleotides. Biochemical data indicate is inefficient forward translocation cleavage. These findings suggest transcription prone incapable hydrolysis, ensuring efficient dsRNA production by IV–RDR2.

Language: Английский

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NusG–Spt5 Transcription Factors: Universal, Dynamic Modulators of Gene Expression

Journal of Molecular Biology, Journal Year: 2024, Volume and Issue: unknown, P. 168814 - 168814

Published: Oct. 1, 2024

The accurate and efficient biogenesis of RNA by cellular polymerase (RNAP) requires accessory factors that regulate the initiation, elongation, termination transcription. Of many discovered to date, elongation regulator NusG-Spt5 is only universally conserved transcription factor. With orthologs paralogs found in all three domains life, this ubiquity underscores their ancient essential regulatory functions. proteins evolved maintain a similar binding interface RNAP through contacts NusG N-terminal domain (NGN) bridge main DNA-binding cleft. We propose varying strength these contacts, modulated tethering interactions, either decrease transcriptional pausing smoothing rugged thermodynamic landscape transcript or enhance pausing, depending on which conformation stabilized NGN contacts. contains one (in bacteria archaea) more eukaryotes) C-terminal use KOW fold contact diverse targets, tether NGN, control biogenesis. Recent work highlights functions different organisms. Some contain multiple specialized subsets operons via sequence-specific targeting, controlling production antibiotics, toxins, capsule proteins. Despite common origin, can differ target selection, interacting partners, effects synthesis. describe current understanding structure, interactions with other regulators, including significant recent progress from genome-wide analyses, single-molecule visualization, cryo-EM. findings highlight remarkable diversity function among structurally

Language: Английский

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Assembly of the Xrn2/Rat1–Rai1–Rtt103 termination complexes in mesophilic and thermophilic organisms

Structure, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 1, 2024

Language: Английский

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How is polyadenylation restricted to 3′‐untranslated regions?

Yeast, Journal Year: 2023, Volume and Issue: 41(4), P. 186 - 191

Published: Dec. 2, 2023

Polyadenylation occurs at numerous sites within 3'-untranslated regions (3'-UTRs) but rarely coding regions. How does Pol II travel through long without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3'-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3'-UTRs, is unknown how its recruitment restricted to 3'-UTRs during elongation. Unlike regions, have AT-rich stretches of DNA that may be important for restricting 3'-UTRs. Recognition 3'-UTR could occur (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA- and/or rA:dT-rich) level. Based on nucleic acid critical recognition, there are three classes models, not mutually exclusive, CpA selectively recruited thereby where occurs: (1) RNA-based models suggest complex directly (or indirectly one more intermediary proteins) binds AU-rich exposed after passes these (2) DNA-based sequence affects nucleosome depletion elongating machinery, resulting in dissociation some elongation factors and subsequent machinery. (3) preferential destabilization rU:dA- rA:dT-rich duplexes bridging nucleotide addition exit association Experiments provide evidence suggested.

Language: Английский

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Zc3h4/Restrictor Exerts a Stranglehold on Unproductive Transcription

Published: Jan. 1, 2024

The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands diseases. In humans, RNAPII transcribes ~25000 protein-coding genes engages apparently futile non-coding at other sites. Despite being so ubiquitous, this usually attenuated soon after initiation the resulting products are immediately degraded nuclear exosome. We others have recently described a new complex, termed "Restrictor", which plays role controlling such unproductive transcription. Underpinned binding protein, ZC3H4, Restrictor curtails genome-wide essential for mammalian development. Here, we discuss these recent discoveries speculate on some many unknowns regarding function mechanism.

Language: Английский

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